Problems with Render Layers
One thing - disabling Eye icon in Outliner Editor hides object from viewport not from Rendering, for that you have to enable Render (Camera) icon in filtering. 

Disableing these objects from rendering will affect both Layers. To fix it you have to place them into separate Collection (I called it "Scene"). Like that you can disable it for one layer and keep in others by switching checkbox of collection.




Second thing - To add additional Lights with Glare in compositor I would use rather enable Film > Transparency and in compositor use Alpha socket as input. Alpha because even you disable whole Scene collection you still use world light that will affect compositing. Like that you can also save one Mix node from tree to get same result.